Brent Pedersen

Hi, I'm not sure how to help with this exact issue, but there's a problem with your pysam install, you might try re-installing pysam in that environment.

I would check the pysam issues and/or ask there.

Hi, can you show me where to find this? I looked in this one: https://storage.googleapis.com/gcp-public-data--gnomad/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.sites.chrY.vcf.bgz and don't see those values

The spec: https://samtools.github.io/hts-specs/VCFv4.2.pdf says: ``` 1.2 Meta-information lines File meta-information is included after the ## string and must be key=value pairs. ``` So, I get that you want more lenient...

I would suggest to use the duphold values like DHFFC for filtering rather than SHQ. But if you do want to use it, can you share a variant so I...

Hi, your sample is not HET so the value is -1. But smoove also requires other fields: https://github.com/brentp/smoove/blob/master/annotate/annotate.go#L349-L377 you probably need to run smoove call with the `--genotype` flag.

you have "smoothe" instead of "smoove"

you only need to run `smoove call --genotype` do not run the lumpy_cmd.sh, that is run by smoove and when you run it, you overwrite the output of smoove.

``` gsort and bcftools required for svtyper ``` so it is not able to genotype. you must install those.

hi, are you sure you indexed with bwa mem2? it looks like you indexed only with bwa mem